diff --git a/Manifest.toml b/Manifest.toml
index 3dd7435fcfb4200b13b1b8e756002f8e20c6de07..74690b3e58fab18085d329575fef7b50042e1397 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -1037,11 +1037,11 @@ version = "0.3.3"
[[deps.PlanarLarvae]]
deps = ["DelimitedFiles", "HDF5", "JSON3", "LinearAlgebra", "MAT", "Meshes", "OrderedCollections", "Random", "SHA", "StaticArrays", "Statistics", "StatsBase", "StructTypes"]
-git-tree-sha1 = "6b2dc28d56bcef101672cbf2bb784bbd5d88d579"
+git-tree-sha1 = "d964d040e319fe3bd9140e5bf91d648de6acc96f"
repo-rev = "main"
repo-url = "https://gitlab.pasteur.fr/nyx/PlanarLarvae.jl"
uuid = "c2615984-ef14-4d40-b148-916c85b43307"
-version = "0.15.0"
+version = "0.16.0"
[[deps.PlotUtils]]
deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"]
diff --git a/Project.toml b/Project.toml
index 7041c66a1c027cc90344a8ba2d6347be9df2f656..8fb6e4f15ce38d27ccbeb2e40db042577ce8ef3b 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
name = "LarvaTagger"
uuid = "8b3b36f1-dfed-446e-8561-ea19fe966a4d"
authors = ["François Laurent", "Institut Pasteur"]
-version = "0.17.1"
+version = "0.18"
[deps]
Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
diff --git a/recipes/Dockerfile b/recipes/Dockerfile
index f73b1b4a5d03ac91969225027e82e040ee583406..c09163d71126f2024fcf6912d9d8f9814eb87c0b 100644
--- a/recipes/Dockerfile
+++ b/recipes/Dockerfile
@@ -77,6 +77,7 @@ RUN if [ -z $TAGGINGBACKENDS_BRANCH ]; then \
&& git clone --depth 1 --no-tags --single-branch -b $(echo $BACKEND | cut -d/ -f2) https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA \
&& cd MaggotUBA \
&& rm -rf .git \
+ && (cat requirements.txt | xargs -I % sh -c 'poetry add "%"') \
&& poetry install --only main \
&& poetry add "pynvml==11.4.1" \
&& if [ "$(echo $BACKEND | cut -d/ -f2)" = "main" ] || [ "$(echo $BACKEND | cut -d/ -f2)" = "dev" ]; then \
diff --git a/recipes/README.md b/recipes/README.md
index 19d5223a5cc57eaf46a98d4caf505d6389c8b145..d13b72db0b1b1172fbff13c419ee060b7ca702cd 100644
--- a/recipes/README.md
+++ b/recipes/README.md
@@ -173,7 +173,7 @@ docker pull flaur/larvatagger
```
Beware that images that ship with a tagging backend are relatively large files (>5GB on disk).
-If you are not interested in automatic tagging, use the `flaur/larvatagger:0.17.1-standalone` image instead.
+If you are not interested in automatic tagging, use the `flaur/larvatagger:0.18-standalone` image instead.
### Upgrading
diff --git a/test/deploy_and_test.sh b/test/deploy_and_test.sh
index 4d3ca51c7c3f1c59d122a296b6a3df53a4ea53f6..45c5a8dfc874ddd2bea4c00bff80eb3f06db634f 100755
--- a/test/deploy_and_test.sh
+++ b/test/deploy_and_test.sh
@@ -37,7 +37,7 @@ if ! julia -v &> /dev/null; then
# do NOT use juliaup to install Julia
module load Python &> /dev/null # Maestro
python3 -m pip install jill
- python3 -m jill install -v 1.9.1 -c
+ python3 -m jill install -v 1.10.0 -c
fi
# h5diff (for tests) on Maestro
@@ -82,7 +82,7 @@ ln -s $(realpath MaggotUBA-adapter) MaggotUBA
# the step below may not be necessary
(cd TaggingBackends && JULIA_PROJECT=$(pwd) poetry run python -c 'import julia; julia.install()')
-(cd MaggotUBA && poetry env use python3.8 && poetry install -v && poetry remove taggingbackends && poetry add ../TaggingBackends && scripts/make_models.jl default)
+(cd MaggotUBA && poetry env use python3.8 && (cat requirements.txt | xargs -I % sh -c 'poetry add "%"') && poetry install -v && poetry remove taggingbackends && poetry add ../TaggingBackends && scripts/make_models.jl default)
cd LarvaTagger || exit 1
julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.develop(path="../PlanarLarvae")'
@@ -97,7 +97,7 @@ if [ -f ../../LarvaTagger_test_data.tgz ]; then
# KEEP_MODEL_FILES=1 ./deploy_and_test.sh
# cd LarvaTagger/LarvaTagger.jl
# rm -rf test/data/test_train_*
- # cp -ra ../MaggotUBA/models/test_train_* test/data/
+ # cp -Rp ../MaggotUBA/models/test_train_* test/data/
# tar zcvf LarvaTagger_test_data.tgz test/data/*
# mv LarvaTagger_test_data.tgz ../../
tar zxvf ../../LarvaTagger_test_data.tgz
diff --git a/test/scenarii.sh b/test/scenarii.sh
index cfe2784ad504372ec4396e644b400137203a0839..2d4c31022437bdd616878ae7e24f29cf9f28ff11 100755
--- a/test/scenarii.sh
+++ b/test/scenarii.sh
@@ -50,9 +50,10 @@ endTest() {
prepareTestData() {
tmpdir="$SHUNIT_TMPDIR/$1"
+ shift
rm -rf "$tmpdir"
mkdir -p "$tmpdir"
- for file in sample.spine sample.outline; do
+ for file in sample.spine sample.outline $@; do
cp "$datapath/$file" "$tmpdir/" || exit 1
done
echo $tmpdir
@@ -123,6 +124,33 @@ testPredictDefault() {
endTest
}
+# requires: sample.spine sample.outline trx.mat original_predictions.label test_train_default/predicted.label
+testPredictWithConflictingInput() {
+ tagger="test_train_default$tagger_suffix"
+ # make test data
+ touch "$datapath/spurious.txt"
+ tmpdir=$(prepareTestData $tagger trx.mat original_predictions.label spurious.txt)
+ # restore the model
+ mkdir -p "$maggotuba/models"
+ rm -rf "$maggotuba/models/$tagger"
+ echo "cp -Rp \"$datapath/$tagger\" \"$maggotuba/models/\""
+ cp -Rp "$datapath/$tagger" "$maggotuba/models/"
+ [ -f "$maggotuba/models/$tagger/clf_config.json" ] || exit 1
+ # run
+ cd "$project_root"
+ echo "\"$larvataggerjl\" predict \"$maggotuba\" $tagger \"$tmpdir\" --debug"
+ "$larvataggerjl" predict "$maggotuba" $tagger "$tmpdir" --debug
+ # compare
+ filename=predicted.label
+ predictions="$tmpdir/$filename"
+ expected_labels="$datapath/$tagger/$filename"
+ assertFalse "\`predict\` failed to generate file $filename" '[ -z "$predictions" ]'
+ assertTrue "\`predict\` failed to reproduce file $filename" '$(cmp "$expected_labels" "$predictions")'
+ # clean up
+ rm -f "$datapath/spurious.txt"
+ endTest
+}
+
# requires: sample.spine sample.outline original_predictions.label test_train_default/*
testTrainDefault() {
tagger="test_train_default$tagger_suffix"
@@ -238,7 +266,7 @@ postTrain() {
assertTrue "\`train\` failed to reproduce file $enc_weights" '$(cmp "$expected_tagger_dir/$enc_weights" "$enc_weights_path")'
assertTrue "\`train\` failed to reproduce file $enc_config" '$(cmp "$expected_tagger_dir/$enc_config" "$enc_config_path")'
assertTrue "\`train\` failed to reproduce file $clf_weights" '$(cmp "$expected_tagger_dir/$clf_weights" "$clf_weights_path")'
- assertTrue "\`train\` failed to reproduce file $clf_config" '$(cmp "$expected_tagger_dir/$clf_config" "$clf_config_path")'
+ assertTrue "\`train\` failed to reproduce file $clf_config" '[ -z "$(diff "$expected_tagger_dir/$clf_config" "$clf_config_path" | grep -E "^[<>] " | grep -vE larva_dataset_.*[.]hdf5)" ]'
# test the predictions
echo "\"$larvataggerjl\" predict \"$maggotuba\" $tagger \"$tmpdir/sample.spine\""